Just a simple request i'd like to see added for modders. Allow planetary improvements to have penalties and not just bonuses. Currently, negative values in the bonus tags are ignored. The reason for this is that it would open up many more options for modded improvements. A modder could add factories with higher than equivalent production at the cost of population growth and/or morale or Bars the boost morale and income but reduce the planets social and/or military production bonus.
I'm not sure what underlying problems this could cause, so simple may actually be rather complex. The tech tree supports these kinds of negative bonuses but they are applied to a players ability, and not on an individual planet scale. Even using the tech tree for penalties has potential problems (in 1.0x atleast) if the bonus is reduced too much (from crashing to rolling over, though the way v1.1 handles bonuses may resolve all or part of these quirks), but that's something modders need to take into consideration.